Current approaches for identifying functional nucleic acids and small molecules from libraries of such molecules are generally indirect. They require the synthesis of tagged substrates and typically involve multiple manipulations. Thus, current approaches leave much to be desired for the efficient screening of libraries of rapidly increasing complexity.
In vitro selection is a key component of efforts to discover functional nucleic acids and small molecules from libraries of DNA, RNA, and small molecules. (1) When the desired activity is binding affinity, as is the case for aptamer evolution (2) or for the discovery of DNA-linked small molecules that bind to a particular target, (3) a direct selection is possible; the library is typically incubated with immobilized target molecules, and bound library members are washed and eluted before being subjected to PCR amplification (FIG. 1a).
In vitro selections have also been developed to evolve RNA and DNA catalysts (4) and, more recently, to discover new reactions from DNA-encoded libraries of potential substrates. (5) In these selections, library members may undergo bond formation or bond cleavage. Selections for reactivity are significantly more complicated than selections for binding affinity. Typically, libraries are incubated with biotinylated substrates or potential reaction partners. Bond formation results in the attachment of biotin to a library member, which in turn enables its capture by immobilized avidin (FIG. 1b). (6) For bond cleavage, an inverse approach is commonly used in which immobilized, biotinylated library members are liberated upon bond scission. (7) While effective, such selections for chemical reactivity are indirect, require the synthesis of biotin-linked substrates, and involve multiple solution-phase and/or solid-phase manipulations. Therefore, better approaches to selection for chemical reactivity are needed to more efficiently screen complex libraries of chemical compounds for the discovery of new chemical reactions and interactions. References (1)-(7) are identified in Example 1.